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Yorodumi- PDB-2yq9: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yq9 | |||||||||
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Title | Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation V321A, crystallized with 2'-AMP | |||||||||
Components | 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE | |||||||||
Keywords | HYDROLASE / MYELIN / NERVOUS SYSTEM | |||||||||
Function / homology | Function and homology information cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / axonogenesis / adult locomotory behavior / cell projection / response to toxic substance / melanosome / myelin sheath / mitochondrial inner membrane / microtubule / mitochondrial outer membrane / response to lipopolysaccharide / perinuclear region of cytoplasm / extracellular space / RNA binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Myllykoski, M. / Raasakka, A. / Lehtimaki, M. / Han, H. / Kursula, P. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Crystallographic Analysis of the Reaction Cycle of 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family Authors: Myllykoski, M. / Raasakka, A. / Lehtimaki, M. / Han, H. / Kursula, I. / Kursula, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yq9.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yq9.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/2yq9 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/2yq9 | HTTPS FTP |
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-Related structure data
Related structure data | 2yozC 2yp0C 2ypcC 2ypeC 2yphC 3zbrC 3zbsC 3zbzC 2xmiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24265.875 Da / Num. of mol.: 1 / Fragment: C-TERMINAL CATALYTIC DOMAIN, RESIDUES 159-378 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PTH 27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase |
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#2: Chemical | ChemComp-2AM / |
#3: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL GLYCINE REMAINS FROM TEV-CLEAVAGE OF EXPRESSION TAG. RESIDUE NUMBERING IS ACCORDING TO ...N-TERMINAL GLYCINE REMAINS FROM TEV-CLEAVAGE OF EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.7 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 4 Details: 250 UM PROTEIN AND 10 MM 23-CYCLIC AMP WERE MIXED IN 0.5 PLUS 0.5 DROPS WITH 50 MM SODIUM ACETATE (1:2 PH3:PH5) AND 25% PEG 4000 IN 4C TEMP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04088 |
Detector | Type: MARRESEARCH MX-165 / Detector: CCD / Date: Feb 2, 2012 Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M) |
Radiation | Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04088 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 16784 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 23.81 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.5 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XMI Resolution: 1.9→28.426 Å / SU ML: 0.21 / σ(F): 2.01 / Phase error: 23.26 / Stereochemistry target values: ML Details: HYDROGENS WERE INCLUDED IN RIDING POSITION. RESIDUES 158-161 AND 209-212 WERE NOT MODELED DUE TO INSUFFICIENT ELECTRON DENSITY.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.426 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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